I have a processing stream that outputs both ingots of various metals and clay/quartz and if I enable the 'try 3x3 first' mode [so it can accept the 2x2 for the clay and quartz] it keeps making iron trapdoors.

If there is a 3x3 recipe I think it should not process the corresponding 2x2 recipe even if there are fewer than 9 items in the input.